<br><br><div class="gmail_quote">On Mon, Nov 30, 2009 at 11:44 AM, Victor Rühle <span dir="ltr"><<a href="mailto:ruehle@mpip-mainz.mpg.de">ruehle@mpip-mainz.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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p.s.: in the dev branch, the file molfile_plugin.h is not copied during installation</blockquote><div><br>why does this matter?<br>This file is a VMD include file and only included in the GROMACS source to avoid a dependency on VMD at compile time. But it is not an external interface to GROMACS. So I don't know why anyone would need that include file. <br>
<br>Roland<br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5"><br>
<br>
Berk Hess wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
We can't do that, since these numbers have to match the contents of the<br>
moltype entry.<br>
<br>
Berk<br>
<br>
Victor Rühle wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Berk,<br>
<br>
thanks for the quick answer. The only thing I don't understand then is<br>
the t_block structure mtop.mols which contains at least the correct<br>
partitioning of atoms into molecules (also in the old tpr files).<br>
<br>
Since this data is there, wouldn't it be better to initialize the<br>
mtop.nmolblock.natoms_mol + mtop.nmolblock.nmol accordingly?<br>
<br>
Victor<br>
<br>
Berk Hess wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br>
<br>
The old tpr files do not contain information on molecular topologies,<br>
so the only thing we can do is consider the whole system as one large<br>
moleculetype.<br>
<br>
Berk<br>
<br>
Victor Rühle wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear all,<br>
<br>
I changed my code for reading .tpr files to read_tpx to get molecule<br>
names. When I use the tpr-file generated by a recent gromacs version,<br>
everything works fine.<br>
<br>
However when using older .tpr files (before molecule names were<br>
stored), there is an inconsistency in the structures:<br>
<br>
mtop.nmolblock = 1<br>
mtop.nmoltype = 1<br>
<br>
mtop.molblock[0].nmol = 1<br>
<a href="http://mtop.mols.nr" target="_blank">mtop.mols.nr</a> = real number of molecules<br>
<br>
Is this a bug or a feature? As one can see, at least some molecule<br>
information is still there but just the new structures are not set up<br>
properly. If I run tpbconv, it puts all atoms in a single molecule.<br>
<br>
Possible workarounds are to rerun grompp to create new tpr files or<br>
change my read function to compensate for this problem. Both solutions<br>
are not very nice.<br>
<br>
Did anybody else had a similar problem?<br>
<br>
Thanks for your help,<br>
Victor<br>
</blockquote></blockquote></blockquote>
<br>
</blockquote>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>